festim-dev · RemDelaporteMathurin · Jul 4, 2024 · Jul 4, 2024 · Jul 4, 2024 · Jul 4, 2024
diff --git a/docs/source/api/boundary_conditions.rst b/docs/source/api/boundary_conditions.rst
@@ -1,12 +1,11 @@
+.. _boundary_conditions_api:
+
+===================
 Boundary conditions
 ===================
 
 .. currentmodule:: festim
 
-
-Dirichlet
----------
-
 .. autoclass:: DirichletBC
     :members:
     :show-inheritance:
@@ -27,10 +26,6 @@ Dirichlet
     :members:
     :show-inheritance:
 
-
-Flux
-----
-
 .. autoclass:: FluxBC
     :members:
     :show-inheritance:

diff --git a/docs/source/api/materials.rst b/docs/source/api/materials.rst
@@ -1,3 +1,5 @@
+.. _materials_api:
+
 Materials
 =========
 

diff --git a/docs/source/api/sources.rst b/docs/source/api/sources.rst
@@ -1,3 +1,5 @@
+.. _sources_api:
+
 Sources
 =======
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -62,6 +62,8 @@
     "sphinxcontrib.images",
 ]
 
+suppress_warnings = ["autosectionlabel.*"]
+
 napoleon_use_ivar = True  # needed to correctly format class attributes
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/docs/source/devguide/index.rst b/docs/source/devguide/index.rst
@@ -20,8 +20,6 @@ And/or contribute to the source code by:
 * Fixing bugs
 * Implementing new features
 
-.. _contributing to the code:
-
 ------------------------
 Contributing to the code
 ------------------------

diff --git a/docs/source/theory.rst b/docs/source/theory.rst
@@ -1,5 +1,3 @@
-.. _theory:
-
 ======
 Theory
 ======

diff --git a/docs/source/userguide/beginners_guide.rst b/docs/source/userguide/beginners_guide.rst
@@ -23,7 +23,7 @@ If you're having an issue, the best way to find help is to join the `FESTIM disc
 Install FESTIM
 --------------
 
-Follow the :ref:`installation instructions<Install>` to install FESTIM on your computer.
+Follow the :ref:`installation instructions<Installation>` to install FESTIM on your computer.
 
 ------------------------
 Your first FESTIM script

diff --git a/docs/source/userguide/boundary_conditions.rst b/docs/source/userguide/boundary_conditions.rst
@@ -1,4 +1,5 @@
-.. _boundary conditions:
+.. _boundary_conditions_guide:
+
 ===================
 Boundary conditions
 ===================

diff --git a/docs/source/userguide/index.rst b/docs/source/userguide/index.rst
@@ -3,7 +3,6 @@ User's Guide
 ============
 
 .. toctree::
-   :numbered:
    :maxdepth: 1
 
    beginners_guide

diff --git a/docs/source/userguide/materials.rst b/docs/source/userguide/materials.rst
@@ -1,3 +1,5 @@
+.. _materials_guide:
+
 =========
 Materials
 =========

diff --git a/docs/source/userguide/sources.rst b/docs/source/userguide/sources.rst
@@ -1,4 +1,4 @@
-.. _sources:
+.. _sources_guide:
 
 =======
 Sources

diff --git a/docs/source/userguide/troubleshooting.rst b/docs/source/userguide/troubleshooting.rst
@@ -32,10 +32,9 @@ This will provide more information during the solving stage.
     my_model.log_level = 20
 
 From there, depending on the behaviour of the solver, you can try the following:
-- if the solver diverges, try reducing the time step and/or mesh refinement. It is often
- helpful to inspect the fields to see if there are any obvious issues (like lack of refinement).
-- If the solver converges to a value above the tolerance, try increasing the tolerance.
-Sometimes, the absolute tolerance is too low for the problem at hand, especially when dealing with large numbers.
+
+- if the solver diverges, try reducing the time step and/or mesh refinement. It is often helpful to inspect the fields to see if there are any obvious issues (like lack of refinement).
+- If the solver converges to a value above the tolerance, try increasing the tolerance. Sometimes, the absolute tolerance is too low for the problem at hand, especially when dealing with large numbers.
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/festim/boundary_conditions/dirichlets/sieverts_bc.py b/festim/boundary_conditions/dirichlets/sieverts_bc.py
@@ -12,10 +12,10 @@ class SievertsBC(DirichletBC):
     """Subclass of DirichletBC for Sievert's law
 
     Args:
-    surfaces (list or int): the surfaces of the BC
-    S_0 (float): Sievert's constant pre-exponential factor (m-3/Pa0.5)
-    E_S (float): Sievert's constant activation energy (eV)
-    pressure (float or sp.Expr): hydrogen partial pressure (Pa)
+        surfaces (list or int): the surfaces of the BC
+        S_0 (float): Sievert's constant pre-exponential factor (m-3/Pa0.5)
+        E_S (float): Sievert's constant activation energy (eV)
+        pressure (float or sp.Expr): hydrogen partial pressure (Pa)
     """
 
     def __init__(self, surfaces, S_0, E_S, pressure) -> None:

diff --git a/festim/concentration/traps/extrinsic_trap.py b/festim/concentration/traps/extrinsic_trap.py
@@ -140,7 +140,7 @@ def create_form_density(self, dx, dt, T):
             T (festim.Temperature): the temperature of the
                 simulation
 
-        Notes:
+        .. note::
             T is an argument, although is not used in the formulation of
             extrinsic traps, but potential for subclasses of extrinsic traps
         """

diff --git a/festim/concentration/traps/trap.py b/festim/concentration/traps/trap.py
@@ -20,7 +20,7 @@ class Trap(Concentration):
     Raises:
         ValueError: if duplicates are found in materials
 
-    Notes:
+    .. note::
         Should multiple traps in muliple materials be used, to save on
         dof's, traps can be conglomerated and described in lists in the
         format::

diff --git a/festim/exports/derived_quantities/average_surface.py b/festim/exports/derived_quantities/average_surface.py
@@ -20,7 +20,7 @@ class AverageSurface(SurfaceQuantity):
         function (dolfin.function.function.Function): the solution function of
             the field
 
-    Notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
 
     """

diff --git a/festim/exports/derived_quantities/average_volume.py b/festim/exports/derived_quantities/average_volume.py
@@ -20,7 +20,7 @@ class AverageVolume(VolumeQuantity):
         function (dolfin.function.function.Function): the solution function of
             the field
 
-    Notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
     """
 

diff --git a/festim/exports/derived_quantities/hydrogen_flux.py b/festim/exports/derived_quantities/hydrogen_flux.py
@@ -17,7 +17,7 @@ class HydrogenFlux(SurfaceFlux):
         function (dolfin.function.function.Function): the solution function of
             the hydrogen solute field
 
-    Notes:
+    .. note::
         units are in H/m2/s in 1D, H/m/s in 2D and H/s in 3D domains
 
     """

diff --git a/festim/exports/derived_quantities/maximum_surface.py b/festim/exports/derived_quantities/maximum_surface.py
@@ -20,7 +20,7 @@ class MaximumSurface(SurfaceQuantity):
         function (dolfin.function.function.Function): the solution function of
             the field
 
-    Notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
 
     """

diff --git a/festim/exports/derived_quantities/maximum_volume.py b/festim/exports/derived_quantities/maximum_volume.py
@@ -20,7 +20,7 @@ class MaximumVolume(VolumeQuantity):
         function (dolfin.function.function.Function): the solution function for
             the field
 
-    notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
 
     """

diff --git a/festim/exports/derived_quantities/minimum_surface.py b/festim/exports/derived_quantities/minimum_surface.py
@@ -20,7 +20,7 @@ class MinimumSurface(SurfaceQuantity):
         function (dolfin.function.function.Function): the solution function of
             the field
 
-    Notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
 
     """

diff --git a/festim/exports/derived_quantities/minimum_volume.py b/festim/exports/derived_quantities/minimum_volume.py
@@ -20,7 +20,7 @@ class MinimumVolume(VolumeQuantity):
         function (dolfin.function.function.Function): the solution function for
             the field
 
-    notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
 
     """

diff --git a/festim/exports/derived_quantities/point_value.py b/festim/exports/derived_quantities/point_value.py
@@ -18,7 +18,7 @@ class PointValue(DerivedQuantity):
         function (dolfin.function.function.Function): the solution function of
             the field
 
-    Notes:
+    .. note::
         Units are in H/m3 for hydrogen concentration and K for temperature
 
     """

diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
@@ -21,7 +21,7 @@ class SurfaceFlux(SurfaceQuantity):
         function (dolfin.function.function.Function): the solution function of
             the field
 
-    Notes:
+    .. note::
         Object to compute the flux J of a field u through a surface
         J = integral(+prop * grad(u) . n ds)
         where prop is the property of the field (D, thermal conductivity, etc)
@@ -96,7 +96,8 @@ class SurfaceFluxCylindrical(SurfaceFlux):
     ds is the surface measure in cylindrical coordinates.
     ds = r dr dtheta or ds = r dz dtheta
 
-    Note: for particle fluxes J is given in H/s, for heat fluxes J is given in W
+    .. note::
+        For particle fluxes J is given in H/s, for heat fluxes J is given in W
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
@@ -172,7 +173,8 @@ class SurfaceFluxSpherical(SurfaceFlux):
     ds is the surface measure in spherical coordinates.
     ds = r^2 sin(theta) dtheta dphi
 
-    Note: for particle fluxes J is given in H/s, for heat fluxes J is given in W
+    .. note::
+        For particle fluxes J is given in H/s, for heat fluxes J is given in W
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")

diff --git a/festim/exports/derived_quantities/thermal_flux.py b/festim/exports/derived_quantities/thermal_flux.py
@@ -17,7 +17,7 @@ class ThermalFlux(SurfaceFlux):
         function (dolfin.function.function.Function): the solution function of
             the temperature field
 
-    Notes:
+    .. note::
         units are in W/m2 in 1D, W/m in 2D and W in 3D domains
 
     """

diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
@@ -21,7 +21,7 @@ class TotalSurface(SurfaceQuantity):
         function (dolfin.function.function.Function): the solution function of
             the hydrogen solute field
 
-    Notes:
+    .. note::
         units are in H/m2 in 1D, H/m in 2D and H in 3D domains for hydrogen
         concentration and K in 1D, K m in 2D and K m2 in 3D domains for temperature
 

diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
@@ -21,7 +21,7 @@ class TotalVolume(VolumeQuantity):
         function (dolfin.function.function.Function): the solution function of
             the hydrogen solute field
 
-    Notes:
+    .. note::
         units are in H/m2 in 1D, H/m in 2D and H in 3D domains for hydrogen
         concentration and K m in 1D, K m2 in 2D and K m3 in 3D domains for temperature
-Original file line number
+Diff line change
@@ -1,3 +1,5 @@
+    .. _sources_api:
     Sources
     =======
@@ Expand Down @@